1DGI Virus Receptor date Nov 24, 1999
title Cryo-Em Structure Of Human Poliovirus(Serotype 1)Complexed W Domain Cd155
authors Y.He, V.D.Bowman, S.Mueller, C.M.Bator, J.Bella, X.Peng, T.S.Baker E.Wimmer, R.J.Kuhn, M.G.Rossmann
compound source
Molecule: Poliovirus Receptor
Chain: R
Fragment: Three Extracellular Domains Of Cd155
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Kidney Cells

Molecule: Vp1
Chain: 1
Engineered: Yes

Organism_scientific: Human Poliovirus 1
Organism_taxid: 12080
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hela Cells

Molecule: Vp2
Chain: 2
Engineered: Yes

Organism_scientific: Human Poliovirus 1
Organism_taxid: 12080
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hela Cells

Molecule: Vp3
Chain: 3
Engineered: Yes

Organism_scientific: Human Poliovirus 1
Organism_taxid: 12080
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hela Cells

Molecule: Vp4
Chain: 4
Fragment: Poliovirus Fragments Vp1,Vp2,Vp3,Vp4
Engineered: Yes

Organism_scientific: Human Poliovirus 1
Organism_taxid: 12080
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hela Cells
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 22.00 Å
ligand MYR enzyme
note 1DGI (Molecule of the Month:pdb20)
Gene
Ontology
ChainFunctionProcessComponent
1, 3, 2


4


Primary referenceInteraction of the poliovirus receptor with poliovirus., He Y, Bowman VD, Mueller S, Bator CM, Bella J, Peng X, Baker TS, Wimmer E, Kuhn RJ, Rossmann MG, Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):79-84. PMID:10618374
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgi.pdb1.gz) 1365 Kb
  • LPC: Ligand-Protein Contacts for 1DGI
  • CSU: Contacts of Structural Units for 1DGI
  • Likely Quarternary Molecular Structure file(s) for 1DGI
  • Retrieve 1DGI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DGI from S2C, [Save to disk]
  • View 1DGI in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1DGI
  • VIPERdb: visual, structural and computational analysis of 1DGI
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DGI, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dgi1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1dgi2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1dgi3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1dgi4_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1dgir_, region R [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dgi] [1dgi_4] [1dgi_1] [1dgi_2] [1dgi_3] [1dgi_R]
  • SWISS-PROT database: [P03300] [P15151]
  • Domain organization of [POLG_POL1M] [PVR_HUMAN] by SWISSPFAM
  • Domain found in 1DGI: [IGv ] by SMART
  • Other resources with information on 1DGI
  • Community annotation for 1DGI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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